Blame the pigs! Just kidding. The Nordic Game conference has confirmed that Inafune can't attend due to Capcom's rules concerning foreign travel during the H1N1 epidemic/pandemic. While it's a regrettable development and is quite disappointing for fans of his franchises, know that he's currently being replaced by Team 17's Martyn Brown (of no relation to Capcom).
This does beg the question: If the H1N1 flu remains as serious as it currently is, does this bode badly for Capcom and other foreign developers who will attend E3? Hopefully not.

Update: After asking Capcom Unity's Twitter page, there's a possibility that the Japanese staff won't be present at E3. While this is still uncertain, you can bet that Capcom of America's staff will be there to pick up any slack.